The striker says despite his best efforts he simply cannot get the best out of himself in the club's new playing style and will now depart for pastures new.
Mario Mandzukic has confirmed he will leave Bayern Munich as a result of his failure to adapt to Pep Guardiola's tactics.
Mandzukic has been linked with a host of Premier League clubs, including Chelsea, after his future with the Bundesliga giants came under scrutiny following the signing of Dortmund striker Robert Lewandowski.
The Croatia international - a regular former boss Jupp Heynckes - was in and out of the side last season and ended the campaign by being dropped for the DFB Pokal final victory over Dortmund.
The 28-year-old striker has now confirmed he is leaving Bayern, and pointed to Guardiola's possession-based style as the primary factor behind that decision.
Mandzukic also revealed he had a meeting with Karl-Heinz Rummenigge in early May, telling the Bayern chief he wanted a move.
"At Bayern it was fantastic. It's a fantastic club. Indeed, until recently I didn't even think about leaving, and especially that it would happen now," he told Sportske novosti.
"Let's be honest, the style Guardiola wants at Bayern doesn't suit me.
"In the first leg against Real in Madrid (in the Champions League), I definitely understood, no matter how much I try, I can't get the best out of myself with this style.
"When it's like that, I don't feel good and it's best for everyone that we part.
"Thanks to the club who offered a contract extension, thanks to Guardiola, who is a great coach, and I wish everyone all the best for the future.
"Bayern and their fans will always be the most beautiful and most emotional story of my career. The time has come for new challenges."
Mandzukic refused to say where his next challenge would be as he prepares to represent Croatia at the World Cup.
He is suspended for Thursday's tournament opener against Brazil, but is sure to face Cameroon and Mexico in Group A.